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UniProtKB - P42206 (GUDD_PSEPU)

Entry version 94 (13 Nov 2019)
Sequence version 1 (01 Nov 1995)
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Protein

Glucarate dehydratase

Gene

gudD

Organism
Pseudomonas putida (Arthrobacter siderocapsulatus)
Status
Reviewed-Annotation score:

Annotation score:3 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Catalyzes the dehydration of glucarate to 5-keto-4-deoxy-D-glucarate (5-kdGluc).

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the ‘Function’ section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Mg2+By similarity

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: D-glucarate degradation

This protein is involved in step 1 of the subpathway that synthesizes 2,5-dioxopentanoate from D-glucarate.
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. Glucarate dehydratase (gudD)
  2. Probable 5-dehydro-4-deoxyglucarate dehydratase (HA62_06375), Probable 5-dehydro-4-deoxyglucarate dehydratase (DW66_3364), Probable 5-dehydro-4-deoxyglucarate dehydratase (kdgD), Probable 5-dehydro-4-deoxyglucarate dehydratase (AO269_10510), Probable 5-dehydro-4-deoxyglucarate dehydratase (BGP84_13810), Probable 5-dehydro-4-deoxyglucarate dehydratase (kdgD), Probable 5-dehydro-4-deoxyglucarate dehydratase (A3L25_25870), Probable 5-dehydro-4-deoxyglucarate dehydratase (kdgD), Probable 5-dehydro-4-deoxyglucarate dehydratase (kdgD), Probable 5-dehydro-4-deoxyglucarate dehydratase (kdgD), Probable 5-dehydro-4-deoxyglucarate dehydratase (PSEMO_05320), Probable 5-dehydro-4-deoxyglucarate dehydratase (kdgD), Probable 5-dehydro-4-deoxyglucarate dehydratase (AYO28_18420), Probable 5-dehydro-4-deoxyglucarate dehydratase (kdgD), Probable 5-dehydro-4-deoxyglucarate dehydratase (SAMN03097715_05359), Probable 5-dehydro-4-deoxyglucarate dehydratase (HB4184_13805), Probable 5-dehydro-4-deoxyglucarate dehydratase (kdgD), Probable 5-dehydro-4-deoxyglucarate dehydratase (KF715C_ch30880), Probable 5-dehydro-4-deoxyglucarate dehydratase (BGP80_16365), Probable 5-dehydro-4-deoxyglucarate dehydratase (BL240_12265), Probable 5-dehydro-4-deoxyglucarate dehydratase (B7H18_17750), Probable 5-dehydro-4-deoxyglucarate dehydratase (kdgD), Probable 5-dehydro-4-deoxyglucarate dehydratase (BIW19_13625), 5-dehydro-4-deoxyglucarate dehydratase, Probable 5-dehydro-4-deoxyglucarate dehydratase (kdgD), Probable 5-dehydro-4-deoxyglucarate dehydratase (kdgD), Probable 5-dehydro-4-deoxyglucarate dehydratase (CBL13_00668), Probable 5-dehydro-4-deoxyglucarate dehydratase (mosA), Probable 5-dehydro-4-deoxyglucarate dehydratase (B8W72_02700), Probable 5-dehydro-4-deoxyglucarate dehydratase (mosA), Probable 5-dehydro-4-deoxyglucarate dehydratase (kdgD), Probable 5-dehydro-4-deoxyglucarate dehydratase (HB13667_24465)
This subpathway is part of the pathway D-glucarate degradation, which is itself part of Carbohydrate acid metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes 2,5-dioxopentanoate from D-glucarate, the pathway D-glucarate degradation and in Carbohydrate acid metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei38SubstrateBy similarity1
Binding sitei109SubstrateBy similarity1
Binding sitei156SubstrateBy similarity1
Binding sitei211SubstrateBy similarity1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei213Proton acceptorBy similarity1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the ‘Description’ field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi241MagnesiumBy similarity1
Metal bindingi272MagnesiumBy similarity1
Metal bindingi295MagnesiumBy similarity1
Binding sitei295SubstrateBy similarity1
Active sitei345Proton acceptorBy similarity1
Binding sitei374SubstrateBy similarity1
Binding sitei427SubstrateBy similarity1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionLyase
LigandMagnesium, Metal-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		MetaCyc:MONOMER-15627

BRENDA Comprehensive Enzyme Information System

More...BRENDAi		4.2.1.40 5092

SABIO-RK: Biochemical Reaction Kinetics Database

More...SABIO-RKi		P42206

UniPathway: a resource for the exploration and annotation of metabolic pathways

More...UniPathwayi		UPA00564;UER00627

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Glucarate dehydratase (EC:4.2.1.40)
Short name:
GDH
Short name:
GlucD
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:gudD
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiPseudomonas putida (Arthrobacter siderocapsulatus)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri303 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteria › Proteobacteria › Gammaproteobacteria › Pseudomonadales › Pseudomonadaceae › Pseudomonas ›

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001712681 – 451Glucarate dehydrataseAdd BLAST451

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homotetramer.

1 Publication

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1451
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...SMRi		P42206

Database of comparative protein structure models

More...ModBasei		Search...

Protein Data Bank in Europe - Knowledge Base

More...PDBe-KBi		Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...EvolutionaryTracei		P42206

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni241 – 243Substrate bindingBy similarity3
Regioni345 – 347Substrate bindingBy similarity3

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the mandelate racemase/muconate lactonizing enzyme family. GlucD subfamily.Curated

Family and domain databases

Conserved Domains Database

More...CDDi		cd03323 D-glucarate_dehydratase, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		3.20.20.120, 1 hit
3.30.390.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR036849 Enolase-like_C_sf
IPR029017 Enolase-like_N
IPR029065 Enolase_C-like
IPR017653 Glucarate_dehydratase
IPR034598 GlucD-like
IPR034593 Mandelate_racemase-like
IPR013342 Mandelate_racemase_C
IPR013341 Mandelate_racemase_N_dom

The PANTHER Classification System

More...PANTHERi		PTHR43287 PTHR43287, 1 hit

Pfam protein domain database

More...Pfami		View protein in Pfam
PF13378 MR_MLE_C, 1 hit
PF02746 MR_MLE_N, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...SMARTi		View protein in SMART
SM00922 MR_MLE, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF51604 SSF51604, 1 hit
SSF54826 SSF54826, 1 hit

TIGRFAMs; a protein family database

More...TIGRFAMsi		TIGR03247 glucar-dehydr, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

P42206-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MEALNQSQAA TGAPVITDLK VVPVAGHDSM LLNLSGAHGP LFTRNILILT 
        60         70         80         90        100
DSSGHVGVGE VPGGEGIRKT LEDARHLLIN QSIGNYQSLL NKVRNAFADR 
       110        120        130        140        150
DVGGRGLQTF DLRIAVHAVT AVESALLDLL GQHLQVPVAA LLGEGQQRDA 
       160        170        180        190        200
VEMLGYLFYV GDRNKTDLGY RSEHEADNEW FRLRNKEALT PESVVALAEA 
       210        220        230        240        250
AYDRYGFKDF KLKGGVLRGE DEIAAVTALS ERFPDARITL DPNGAWSLKE 
       260        270        280        290        300
AVALCRDQHH VLAYAEDPCG AENGYSGREV MAEFRRSTGL RTATNMIATD 
       310        320        330        340        350
WRQMGHAIQL QSVDIPLADP HFWTMQGSVR VAQMCNEWGL TWGSHSNNHF 
       360        370        380        390        400
DISLAMFTHV AAAAPGNITA IDTHWIWQDG QRLTKEPLQI KGGLVEVPKK 
       410        420        430        440        450
PGLGVELDWD ALMKAHEVYK SMGLGARDDA TAMRYLVSGW EFNNKRPCMV 

R
Length:451
Mass (Da):49,572
Last modified:November 1, 1995 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i04CCB563BCB1C6EA
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...EMBLi

GenBank nucleotide sequence database

More...GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...DDBJi
Links Updated
M69160 Genomic DNA Translation: AAA25868.1

Protein sequence database of the Protein Information Resource

More...PIRi		S27617

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M69160 Genomic DNA Translation: AAA25868.1
PIRiS27617

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...PDBei

Protein Data Bank RCSB

More...RCSB PDBi

Protein Data Bank Japan

More...PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1BQGX-ray2.30A1-451[»]
SMRiP42206
ModBaseiSearch...
PDBe-KBiSearch...

Enzyme and pathway databases

UniPathwayiUPA00564;UER00627
BioCyciMetaCyc:MONOMER-15627
BRENDAi4.2.1.40 5092
SABIO-RKiP42206

Miscellaneous databases

EvolutionaryTraceiP42206

Family and domain databases

CDDicd03323 D-glucarate_dehydratase, 1 hit
Gene3Di3.20.20.120, 1 hit
3.30.390.10, 1 hit
InterProiView protein in InterPro
IPR036849 Enolase-like_C_sf
IPR029017 Enolase-like_N
IPR029065 Enolase_C-like
IPR017653 Glucarate_dehydratase
IPR034598 GlucD-like
IPR034593 Mandelate_racemase-like
IPR013342 Mandelate_racemase_C
IPR013341 Mandelate_racemase_N_dom
PANTHERiPTHR43287 PTHR43287, 1 hit
PfamiView protein in Pfam
PF13378 MR_MLE_C, 1 hit
PF02746 MR_MLE_N, 1 hit
SMARTiView protein in SMART
SM00922 MR_MLE, 1 hit
SUPFAMiSSF51604 SSF51604, 1 hit
SSF54826 SSF54826, 1 hit
TIGRFAMsiTIGR03247 glucar-dehydr, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...ProtoNeti		Search...

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiGUDD_PSEPU
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P42206
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1995
Last modified: November 13, 2019
This is version 94 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. PATHWAY comments
    Index of metabolic and biosynthesis pathways
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